AW: [gmx-users] question about the minimization
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Thu Oct 18 12:15:15 CEST 2012
Hi Erik,
my .mdp file looks like this:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 30000
nstenergy = 1
energygrps = System
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
rlist = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
pbc = xyz
And yes, I use constraints. I have a membrane represented by dummy atoms
around my protein. They are fixed and I also fixed the backbone. Or is
that a problem.
Thank you ,
Eva
> It could be due to your mdp-settings. What's your time step? Do you use
> constraints and virtual interaction sites?
>
> Erik
>
> 18 okt 2012 kl. 12.04 skrev reisingere at rostlab.informatik.tu-muenchen.de:
>
>> Hi Felix,
>> thank you for your answer.
>> So you think that a force of 3.2341940e+02 is okey? To work on?
>>
>> I also tried to work on with a NVT run but then I got many many LINCS
>> warnings:
>>
>> Step 1114, time 2.228 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000169, max 0.001796 (between atoms 3480 and 3482)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3480 3482 30.3 0.1090 0.1092 0.1090
>>
>> Step 1121, time 2.242 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000108, max 0.000561 (between atoms 2000 and 2001)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 2002 2005 30.4 0.1090 0.1090 0.1090
>>
>>
>>
>> And in the end there is the error:
>>
>> Fatal error:
>> 11 particles communicated to PME node 2 are more than 2/3 times the
>> cut-off out of the domain decomposit
>> ion cell of their charge group in dimension x.
>>
>>
>> I looked it up on the GROMACS site and it was written there that such a
>> error is caused by a not well equilibrated system.
>>
>> So I thought that the high force might be the reason.
>>
>> What do you think?
>>
>> Thanks again!!
>>
>>
>>> Hi Eva,
>>>
>>> The change in energy in every step became smaller than the machine
>>> precision can represent (as is stated in the output). In other words:
>>> your
>>> system is minimized to a very high degree.
>>> A value of 10 for the Fmax is very low for a system like yours, even
>>> with
>>> a pure protein in water system you probably wouldn't hit this value.
>>> Furthermore, 30.000 steps for a minimization seems pretty high to me.
>>>
>>> Cheers,
>>> Felix
>>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: gmx-users-bounces at gromacs.org
>>> [mailto:gmx-users-bounces at gromacs.org]
>>> Im Auftrag von reisingere at rostlab.informatik.tu-muenchen.de
>>> Gesendet: Donnerstag, 18. Oktober 2012 10:56
>>> An: gmx-users at gromacs.org
>>> Betreff: [gmx-users] question about the minimization
>>>
>>> Hi everybody,
>>>
>>> I have a question about the minimization of my protein. For this
>>> minimization I fixed the backbone and the membrane atoms which around
>>> my
>>> protein.
>>>
>>> I minimized it 30000 steps long but after step 20385 it stops with the
>>> output:
>>>
>>> Steepest Descents converged to machine precision in 20385 steps, but
>>> did
>>> not reach the requested Fmax < 10.
>>> Potential Energy = -8.8805600e+05
>>> Maximum force = 3.2341940e+02 on atom 3050
>>> Norm of force = 2.0930219e+00
>>>
>>> I do not see why it can not reach a lower force.
>>>
>>> I already looked at the structure with Pymol and there I saw that the
>>> atom
>>> 3050 is in a loop and do not interact with any other residue.
>>>
>>> My .mdp file looks like this:
>>>
>>> define = -DPOSRES
>>> integrator = steep
>>> emtol = 10
>>> nsteps = 30000
>>> nstenergy = 1
>>> energygrps = System
>>> coulombtype = PME
>>> rcoulomb = 0.9
>>> rvdw = 0.9
>>> rlist = 0.9
>>> fourierspacing = 0.12
>>> pme_order = 4
>>> ewald_rtol = 1e-5
>>> pbc = xyz
>>>
>>> Do you see a reason why it can not reach a force lower than 10?
>>>
>>> Thank you,
>>> Eva
>>>
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>>
>>
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>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 6688 fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
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